12 files changed, 204 insertions, 31 deletions
diff --git a/doc/direct_mode.mdwn b/doc/direct_mode.mdwn
index 4c2cb2dd7..d3e1067f9 100644
--- a/doc/direct_mode.mdwn
+++ b/doc/direct_mode.mdwn
@@ -9,6 +9,13 @@ understand how to update its working tree.
 
 [[!toc]]
 
+## deprecated
+
+Direct mode is deprecated! Intead, git-annex v6 repositories can simply
+have files that are unlocked and thus can be directly accessed and
+modified. See [[upgrades]] for details about the transition to v6
+repositories.
+
 ## enabling (and disabling) direct mode
 
 Normally, git-annex repositories start off in indirect mode. With some
diff --git a/doc/git-annex-add.mdwn b/doc/git-annex-add.mdwn
index cfeb8a98e..7f796fec1 100644
--- a/doc/git-annex-add.mdwn
+++ b/doc/git-annex-add.mdwn
@@ -11,12 +11,18 @@ git annex add `[path ...]`
 Adds files in the path to the annex. If no path is specified, adds
 files from the current directory and below.
 
-Normally, files that are already checked into git, or that git has been
-configured to ignore will be silently skipped.
-
-If annex.largefiles is configured, and does not match a file that is being
-added, `git annex add` will behave the same as `git add` and add the
-non-large file directly to the git repository, instead of to the annex.
+Files that are already checked into git and are unmodified, or that
+git has been configured to ignore will be silently skipped.
+
+If annex.largefiles is configured, and does not match a file, `git annex
+add` will behave the same as `git add` and add the non-large file directly
+to the git repository, instead of to the annex.
+
+Large files are added to the annex in locked form, which prevents further
+modification of their content unless unlocked by [[git-annex-unlock]](1).
+(This is not the case however when a repository is in direct mode.)
+To add a file to the annex in unlocked form, `git add` can be used instead 
+(that only works when the repository has annex.version 6 or higher).
 
 This command can also be used to add symbolic links, both symlinks to
 annexed content, and other symlinks.
diff --git a/doc/git-annex-direct.mdwn b/doc/git-annex-direct.mdwn
index 457ae3116..3cade1a8c 100644
--- a/doc/git-annex-direct.mdwn
+++ b/doc/git-annex-direct.mdwn
@@ -17,12 +17,18 @@ Note that git commands that operate on the work tree will refuse to
 run in direct mode repositories. Use `git annex proxy` to safely run such
 commands.
 
+Note that the direct mode/indirect mode distinction is removed in v6
+git-annex repositories. In such a repository, you can
+use [[git-annex-unlock]](1) to make a file's content be directly present.
+
 # SEE ALSO
 
 [[git-annex]](1)
 
 [[git-annex-indirect]](1)
 
+[[git-annex-unlock]](1)
+
 # AUTHOR
 
 Joey Hess <id@joeyh.name>
diff --git a/doc/git-annex-indirect.mdwn b/doc/git-annex-indirect.mdwn
index 99def6144..321e0fb36 100644
--- a/doc/git-annex-indirect.mdwn
+++ b/doc/git-annex-indirect.mdwn
@@ -11,9 +11,8 @@ git annex indirect
 Switches a repository back from direct mode to the default, indirect
 mode.
 
-Some systems cannot support git-annex in indirect mode, because they
-do not support symbolic links. Repositories on such systems instead
-default to using direct mode.
+Note that the direct mode/indirect mode distinction is removed in v6
+git-annex repositories.
 
 # SEE ALSO
 
diff --git a/doc/git-annex-init.mdwn b/doc/git-annex-init.mdwn
index 145705105..29522181d 100644
--- a/doc/git-annex-init.mdwn
+++ b/doc/git-annex-init.mdwn
@@ -24,6 +24,13 @@ mark it as dead (see [[git-annex-dead]](1)).
 This command is entirely safe, although usually pointless, to run inside an
 already initialized git-annex repository.
 
+# OPTIONS
+
+* `--version=N`
+
+  Force the repository to be initialized using a different annex.version
+  than the current default.
+
 # SEE ALSO
 
 [[git-annex]](1)
diff --git a/doc/git-annex-lock.mdwn b/doc/git-annex-lock.mdwn
index 4bf279fb2..b9e5d3450 100644
--- a/doc/git-annex-lock.mdwn
+++ b/doc/git-annex-lock.mdwn
@@ -9,7 +9,7 @@ git annex lock `[path ...]`
 # DESCRIPTION
 
 Use this to undo an unlock command if you don't want to modify
-the files, or have made modifications you want to discard.
+the files any longer, or have made modifications you want to discard.
 
 # OPTIONS
 
diff --git a/doc/git-annex-pre-commit.mdwn b/doc/git-annex-pre-commit.mdwn
index bc1e86e18..21e5aef68 100644
--- a/doc/git-annex-pre-commit.mdwn
+++ b/doc/git-annex-pre-commit.mdwn
@@ -12,10 +12,14 @@ This is meant to be called from git's pre-commit hook. `git annex init`
 automatically creates a pre-commit hook using this.
 
 Fixes up symlinks that are staged as part of a commit, to ensure they
-point to annexed content. Also handles injecting changes to unlocked
-files into the annex. When in a view, updates metadata to reflect changes
+point to annexed content.
+
+When in a view, updates metadata to reflect changes
 made to files in the view.
 
+When in a repository that has not been upgraded to annex.version 6, 
+also handles injecting changes to unlocked files into the annex. 
+
 # SEE ALSO
 
 [[git-annex]](1)
diff --git a/doc/git-annex-smudge.mdwn b/doc/git-annex-smudge.mdwn
new file mode 100644
index 000000000..c8e545367
--- /dev/null
+++ b/doc/git-annex-smudge.mdwn
@@ -0,0 +1,47 @@
+# NAME
+
+git-annex smudge - git filter driver for git-annex
+
+# SYNOPSIS
+
+git annex smudge [--clean] file
+
+# DESCRIPTION
+
+This command lets git-annex be used as a git filter driver which lets
+annexed files in the git repository to be unlocked at all times, instead
+of being symlinks.
+
+When adding a file with `git add`, the annex.largefiles config is
+consulted to decide if a given file should be added to git as-is,
+or if its content are large enough to need to use git-annex. To force a
+file that would normally be added to the annex to be added to git as-is,
+this can be temporarily overridden. For example:
+
+	git -c annex.largefiles='exclude=*' add myfile
+
+The git configuration to use this command as a filter driver is as follows.
+This is normally set up for you by git-annex init, so you should
+not need to configure it manually.
+
+	[filter "annex"]
+	        smudge = git-annex smudge %f
+	        clean = git-annex smudge --clean %f
+
+To make git use that filter driver, it needs to be configured in
+the .gitattributes file or in `.git/config/attributes`. The latter
+is normally configured when a repository is initialized, with the following
+contents:
+
+	* filter=annex
+	.* !filter
+
+# SEE ALSO
+
+[[git-annex]](1)
+
+# AUTHOR
+
+Joey Hess <id@joeyh.name>
+
+Warning: Automatically converted into a man page by mdwn2man. Edit with care.
diff --git a/doc/git-annex-unlock.mdwn b/doc/git-annex-unlock.mdwn
index ac8c21185..123146836 100644
--- a/doc/git-annex-unlock.mdwn
+++ b/doc/git-annex-unlock.mdwn
@@ -11,8 +11,16 @@ git annex unlock `[path ...]`
 Normally, the content of annexed files is protected from being changed.
 Unlocking an annexed file allows it to be modified. This replaces the
 symlink for each specified file with a copy of the file's content.
-You can then modify it and `git annex add` (or `git commit`) to inject
-it back into the annex.
+You can then modify it and `git annex add` (or `git commit`) to save your
+changes.
+
+In repositories with annex.version 5 or earlier, unlocking a file is local
+to the repository, and is temporary. With version 6, unlocking a file
+changes how it is stored in the git repository (from a symlink to a pointer
+file), so you can commit it like any other change. Also in version 6, you
+can use `git add` to add a fie to the annex in unlocked form. This allows
+workflows where a file starts out unlocked, is modified as necessary, and
+is locked once it reaches its final version.
 
 # OPTIONS
 
diff --git a/doc/git-annex.mdwn b/doc/git-annex.mdwn
index 2020ccf3f..1a2fd6e67 100644
--- a/doc/git-annex.mdwn
+++ b/doc/git-annex.mdwn
@@ -626,6 +626,14 @@ subdirectories).
 
   See [[git-annex-diffdriver]](1) for details.
 
+* `smudge`
+
+  This command lets git-annex be used as a git filter driver, allowing
+  annexed files in the git repository to be unlocked at all times, instead
+  of being symlinks.
+
+  See [[git-annex-smudge]](1) for details.
+
 * `remotedaemon`
 
   Detects when network remotes have received git pushes and fetches from them.
diff --git a/doc/todo/smudge.mdwn b/doc/todo/smudge.mdwn
index aea0c9b98..e1d54cf7f 100644
--- a/doc/todo/smudge.mdwn
+++ b/doc/todo/smudge.mdwn
@@ -158,7 +158,8 @@ Using git-annex on a crippled filesystem that does not support symlinks.
 Data:
 
 * An annex pointer file has as its first line the git-annex key
-  that it's standing in for. Subsequent lines of the file might
+  that it's standing in for (prefixed with "annex/objects/", similar to
+  an annex symlink target). Subsequent lines of the file might
   be a message saying that the file's content is not currently available.
   An annex pointer file is checked into the git repository the same way
   that an annex symlink is checked in.
@@ -177,8 +178,8 @@ Configuration:
   the annex. Other files are passed through the smudge/clean as-is and
   have their contents stored in git.
 
-* annex.direct is repurposed to configure how the assistant adds files.
-  When set to true, they're added unlocked.
+* annex.direct is repurposed to configure how git-annex adds files.
+  When set to false, it adds symlinks and when true it adds pointer files.
 
 git-annex clean:
 
@@ -232,15 +233,11 @@ git annex lock/unlock:
   transition repositories to using pointers, and a cleaner unlock/lock
   for repos using symlinks.
 
-  unlock will stage a pointer file, and will copy the content of the object
-  out of .git/annex/objects to the work tree file. (Might want a --hardlink
-  switch.)
+  unlock will stage a pointer file, and will link the content of the object
+  from .git/annex/objects to the work tree file.
   
-  lock will replace the current work tree file with the symlink, and stage it.
-  Note that multiple work tree files could point to the same object.
-  So, if the link count is > 1, replace the annex object with a copy of
-  itself to break such a hard link. Always finish by locking down the
-  permissions of the annex object.
+  lock will replace the current work tree file with the symlink, and stage it,
+  and lock down the permissions of the annex object.
 
 #### file map
 
@@ -248,7 +245,8 @@ The file map needs to map from `Key -> [File]`. `File -> Key`
 seems useful to have, but in practice is not worthwhile.
 
 Drop and get operations need to know what files in the work tree use a
-given key in order to update the work tree.
+given key in order to update the work tree. And, we don't want to
+overwrite a work tree file if it's been modified when dropping or getting.
 
 git-annex commands that look at annex symlinks to get keys to act on will
 need fall back to either consulting the file map, or looking at the staged
@@ -275,13 +273,14 @@ In particular:
 * Is the smudge filter called at any other time? Seems unlikely but then
   there could be situations with a detached work tree or such.
 * Does git call any useful hooks when removing a file from the work tree,
-  or converting it to not be annexed?
+  or converting it to not be annexed, or for `git mv` of an annexed file?
   No!
 
 From this analysis, any file map generated by the smudge/clean filters
 is necessary potentially innaccurate. It may list deleted files.
 It may or may not reflect current unstaged changes from the work tree.
 
+
 Follows that any use of the file map needs to verify the info from it,
 and throw out bad cached info (updating the map to match reality). 
 
@@ -306,17 +305,60 @@ just look at the repo content in the first place..
 
 annex.version changes to 6
 
-Upgrade should be handled automatically.
+git config for filter.annex.smudge and filter.annex.clean is set up.
 
-On upgrade, update .gitattributes with a stock configuration, unless
-it already mentions "filter=annex".
+.gitattributes is updated with a stock configuration,
+unless it already mentions "filter=annex".
 
 Upgrading a direct mode repo needs to switch it out of bare mode, and
 needs to run `git annex unlock` on all files (or reach the same result).
 So will need to stage changes to all annexed files.
 
 When a repo has some clones indirect and some direct, the upgraded repo
-will have all files unlocked, necessarily in all clones.
+will have all files unlocked, necessarily in all clones. This happens
+automatically, because when the direct repos are upgraded that causes the
+files to be unlocked, while the indirect upgrades don't touch the files.
+
+#### implementation todo list
+
+* Test suite should have passes for:
+  v5 indirect 
+  v5 direct
+  v6 locked
+  v6 unlocked
+  Currently, the test suite fails horribly.
+* assistant: In v6 mode, adds files in unlocked mode, so they can
+  continue to be modified. TODO
+* When the webapp creates a repo, it forces it into direct mode. But that
+  will fail when annex.version=6. Long-term, the assistant should make v6
+  repos, but short-term, the assistant should make v5 repos in direct mode.
+* Reconcile staged changes into the associated files database, whenever
+  the database is queried.
+* See if the cases where the Keys database is not used can be
+  optimised. Eg, if the Keys database doesn't exist at all,
+  we know smudge/clean are not used, so queries don't
+  need to open the database or do reconciliation, but can simply return none.
+  Also, no need for Backend.lookupFile to catKeyFile in this case
+  (when not in direct mode).
+  However, beware over-optimisation breaking the assistant or perhaps other
+  long-lived processes.
+* Make automatic merge conflict resolution work for pointer files.
+  - Should probably automatically handle merge conflicts between annex
+    symlinks and pointer files too. Maybe by always resulting in a pointer
+    file, since the symlinks don't work everwhere.
+* Crippled filesystem should cause all files to be transparently unlocked.
+  Note that this presents problems when dealing with merge conflicts and
+  when pushing changes committed in such a repo. Ideally, should avoid
+  committing implicit unlocks, or should prevent such commits leaking out
+  in pushes.
+* Dropping a smudged file causes git status to show it as modified, 
+  because the timestamp has changed. Getting a smudged file can also 
+  cause this. Upgrading a direct mode repo also leaves files in this state.
+  User can use `git add` to clear it up, but better to avoid this,
+  by updating stat info in the index.
+  (May need to use libgit2 to do this, cannot find
+  any plumbing except git-update-index, which is very inneficient for
+  smudged files.)
 
 ----
 
diff --git a/doc/upgrades.mdwn b/doc/upgrades.mdwn
index f5e9cbc3a..27f22e16e 100644
--- a/doc/upgrades.mdwn
+++ b/doc/upgrades.mdwn
@@ -43,6 +43,45 @@ conflicts first before upgrading git-annex.
 
 The upgrade events, so far:
 
+## v5 -> v6 (git-annex version 6.x)
+
+The upgrade from v5 to v6 is handled manually. Run `git-annex upgrade`
+perform the upgrade.
+
+Warning: All places that a direct mode repository is cloned to should be 
+running git-annex version 6.x before you upgrade the repository.
+This is necessary because the contents of the repository are changed
+in the upgrade, and the old version of git-annex won't be able to
+access files after the repo is upgraded.
+
+This upgrade does away with the direct mode/indirect mode distinction.
+A v6 git-annex repository can have some files locked and other files
+unlocked, and all git and git-annex commands can be used on both locked and
+unlocked files. (Although for locked files to work, the filesystem
+must support symbolic links..)
+
+The behavior of some commands changes in an upgraded repository:
+
+* `git add` will add files to the annex, in unlocked mode, rather than
+   adding them directly to the git repository. To bypass that and add a file
+   directly to git, use:
+   
+	git -c annex.largefiles='exclude=*' add myfile
+
+* `git annex unlock` and `git annex lock` change how the pointer to 
+  the annexed content is stored in git.
+
+If a repository is only used in indirect mode, you can use git-annex
+v5 and v6 in different clones of the same indirect mode repository without
+problems.
+
+On upgrade, all files in a direct mode repository will be converted to
+unlocked files. The upgrade will stage changes to all annexed files in
+the git repository, which you can then commit.
+
+If a repository has some clones using direct mode and some using indirect
+mode, all the files will end up unlocked in all clones after the upgrade.
+
 ## v4 -> v5 (git-annex version 5.x)
 
 The upgrade from v4 to v5 is handled